1
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Park JG, Jeon H, Shin S, Song C, Lee H, Kim NK, Kim EE, Hwang KY, Lee BJ, Lee IG. Structural basis for CEP192-mediated regulation of centrosomal AURKA. SCIENCE ADVANCES 2023; 9:eadf8582. [PMID: 37083534 PMCID: PMC10121170 DOI: 10.1126/sciadv.adf8582] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Aurora kinase A (AURKA) performs critical functions in mitosis. Thus, the activity and subcellular localization of AURKA are tightly regulated and depend on diverse factors including interactions with the multiple binding cofactors. How these different cofactors regulate AURKA to elicit different levels of activity at distinct subcellular locations and times is poorly understood. Here, we identified a conserved region of CEP192, the major cofactor of AURKA, that mediates the interaction with AURKA. Quantitative binding studies were performed to map the interactions of a conserved helix (Helix-1) within CEP192. The crystal structure of Helix-1 bound to AURKA revealed a distinct binding site that is different from other cofactor proteins such as TPX2. Inhibiting the interaction between Helix-1 and AURKA in cells led to the mitotic defects, demonstrating the importance of the interaction. Collectively, we revealed a structural basis for the CEP192-mediated AURKA regulation at the centrosome, which is distinct from TPX2-mediated regulation on the spindle microtubule.
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Affiliation(s)
- Jin-Gyeong Park
- Biomedical Research Division, Korea Institute of Science and Technology, Seoul 02792, South Korea
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, South Korea
| | - Hanul Jeon
- Biomedical Research Division, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Sangchul Shin
- Technology Support Center, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Chiman Song
- Biomedical Research Division, Korea Institute of Science and Technology, Seoul 02792, South Korea
- Department of Biological Chemistry, University of Science and Technology, Daejeon 34113, South Korea
| | - Hyomin Lee
- Department of Biological Chemistry, University of Science and Technology, Daejeon 34113, South Korea
- Chemical Kinomics Research Center, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Nak-Kyoon Kim
- Advanced Analysis Center, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Eunice EunKyeong Kim
- Biomedical Research Division, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Kwang Yeon Hwang
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, South Korea
| | - Bong-Jin Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, South Korea
| | - In-Gyun Lee
- Biomedical Research Division, Korea Institute of Science and Technology, Seoul 02792, South Korea
- Department of Biological Chemistry, University of Science and Technology, Daejeon 34113, South Korea
- Corresponding author.
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2
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Lee IG, Lee BJ. Aurora Kinase A Regulation by Cysteine Oxidative Modification. Antioxidants (Basel) 2023; 12:antiox12020531. [PMID: 36830089 PMCID: PMC9952272 DOI: 10.3390/antiox12020531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
Aurora kinase A (AURKA), which is a member of serine/threonine kinase family, plays a critical role in regulating mitosis. AURKA has drawn much attention as its dysregulation is critically associated with various cancers, leading to the development of AURKA inhibitors, a new class of anticancer drugs. As the spatiotemporal activity of AURKA critically depends on diverse intra- and inter-molecular factors, including its interaction with various protein cofactors and post-translational modifications, each of these pathways should be exploited for the development of a novel class of AURKA inhibitors other than ATP-competitive inhibitors. Several lines of evidence have recently shown that redox-active molecules can modify the cysteine residues located on the kinase domain of AURKA, thereby regulating its activity. In this review, we present the current understanding of how oxidative modifications of cysteine residues of AURKA, induced by redox-active molecules, structurally and functionally regulate AURKA and discuss their implications in the discovery of novel AURKA inhibitors.
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Affiliation(s)
- In-Gyun Lee
- Biomedical Research Division, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Bong-Jin Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
- Correspondence:
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3
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Xu H. The slow but steady rise of binding free energy calculations in drug discovery. J Comput Aided Mol Des 2023; 37:67-74. [PMID: 36469232 DOI: 10.1007/s10822-022-00494-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
Binding free energy calculations are increasingly used in drug discovery research to predict protein-ligand binding affinities and to prioritize candidate drug molecules accordingly. It has taken decades of collective effort to transform this academic concept into a technology adopted by the pharmaceutical and biotech industry. Having personally witnessed and taken part in this transformation, here I recount the (incomplete) list of problems that had to be solved to make this computational tool practical and suggest areas of future development.
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Affiliation(s)
- Huafeng Xu
- Roivant Discovery, 151 West 42nd Street, New York, NY, 10036, USA.
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4
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Scott DE, Francis-Newton NJ, Marsh ME, Coyne AG, Fischer G, Moschetti T, Bayly AR, Sharpe TD, Haas KT, Barber L, Valenzano CR, Srinivasan R, Huggins DJ, Lee M, Emery A, Hardwick B, Ehebauer M, Dagostin C, Esposito A, Pellegrini L, Perrior T, McKenzie G, Blundell TL, Hyvönen M, Skidmore J, Venkitaraman AR, Abell C. A small-molecule inhibitor of the BRCA2-RAD51 interaction modulates RAD51 assembly and potentiates DNA damage-induced cell death. Cell Chem Biol 2021; 28:835-847.e5. [PMID: 33662256 PMCID: PMC8219027 DOI: 10.1016/j.chembiol.2021.02.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 12/18/2020] [Accepted: 02/03/2021] [Indexed: 12/11/2022]
Abstract
BRCA2 controls RAD51 recombinase during homologous DNA recombination (HDR) through eight evolutionarily conserved BRC repeats, which individually engage RAD51 via the motif Phe-x-x-Ala. Using structure-guided molecular design, templated on a monomeric thermostable chimera between human RAD51 and archaeal RadA, we identify CAM833, a 529 Da orthosteric inhibitor of RAD51:BRC with a Kd of 366 nM. The quinoline of CAM833 occupies a hotspot, the Phe-binding pocket on RAD51 and the methyl of the substituted α-methylbenzyl group occupies the Ala-binding pocket. In cells, CAM833 diminishes formation of damage-induced RAD51 nuclear foci; inhibits RAD51 molecular clustering, suppressing extended RAD51 filament assembly; potentiates cytotoxicity by ionizing radiation, augmenting 4N cell-cycle arrest and apoptotic cell death and works with poly-ADP ribose polymerase (PARP)1 inhibitors to suppress growth in BRCA2-wildtype cells. Thus, chemical inhibition of the protein-protein interaction between BRCA2 and RAD51 disrupts HDR and potentiates DNA damage-induced cell death, with implications for cancer therapy.
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Affiliation(s)
- Duncan E Scott
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Nicola J Francis-Newton
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - May E Marsh
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Anthony G Coyne
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Gerhard Fischer
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Tommaso Moschetti
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Andrew R Bayly
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Timothy D Sharpe
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kalina T Haas
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Lorraine Barber
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Chiara R Valenzano
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Rajavel Srinivasan
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - David J Huggins
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Miyoung Lee
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Amy Emery
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Bryn Hardwick
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Matthias Ehebauer
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Claudio Dagostin
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Alessandro Esposito
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Trevor Perrior
- Excellium Consulting, Brook Farm Barn, Lackford, Bury St Edmunds IP28 6HL, UK
| | - Grahame McKenzie
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
| | - John Skidmore
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Ashok R Venkitaraman
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK.
| | - Chris Abell
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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5
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Ladds MJGW, Popova G, Pastor-Fernández A, Kannan S, van Leeuwen IMM, Håkansson M, Walse B, Tholander F, Bhatia R, Verma CS, Lane DP, Laín S. Exploitation of dihydroorotate dehydrogenase (DHODH) and p53 activation as therapeutic targets: A case study in polypharmacology. J Biol Chem 2020; 295:17935-17949. [PMID: 32900849 PMCID: PMC7939445 DOI: 10.1074/jbc.ra119.012056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 08/18/2020] [Indexed: 01/17/2023] Open
Abstract
The tenovins are a frequently studied class of compounds capable of inhibiting sirtuin activity, which is thought to result in increased acetylation and protection of the tumor suppressor p53 from degradation. However, as we and other laboratories have shown previously, certain tenovins are also capable of inhibiting autophagic flux, demonstrating the ability of these compounds to engage with more than one target. In this study, we present two additional mechanisms by which tenovins are able to activate p53 and kill tumor cells in culture. These mechanisms are the inhibition of a key enzyme of the de novo pyrimidine synthesis pathway, dihydroorotate dehydrogenase (DHODH), and the blockage of uridine transport into cells. These findings hold a 3-fold significance: first, we demonstrate that tenovins, and perhaps other compounds that activate p53, may activate p53 by more than one mechanism; second, that work previously conducted with certain tenovins as SirT1 inhibitors should additionally be viewed through the lens of DHODH inhibition as this is a major contributor to the mechanism of action of the most widely used tenovins; and finally, that small changes in the structure of a small molecule can lead to a dramatic change in the target profile of the molecule even when the phenotypic readout remains static.
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Affiliation(s)
- Marcus J G W Ladds
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Gergana Popova
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Andrés Pastor-Fernández
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | | | | | | | - Fredrik Tholander
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ravi Bhatia
- Division of Hematology and Oncology, O'Neal Comprehensive Cancer Center, University of Alabama, Birmingham, Alabama, USA
| | - Chandra S Verma
- Bioinformatics Institute (BII), A*STAR, Singapore; Department of Biological Sciences, National University of Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore
| | - David P Lane
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sonia Laín
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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6
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Wade AD, Huggins DJ. Identification of Optimal Ligand Growth Vectors Using an Alchemical Free-Energy Method. J Chem Inf Model 2020; 60:5580-5594. [PMID: 32810401 DOI: 10.1021/acs.jcim.0c00610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, a novel method to rationally design inhibitors with improved steric contacts and enhanced binding free energies is presented. This new method uses alchemical single step perturbation calculations to rapidly optimize the van der Waals interactions of a small molecule in a protein-ligand complex in order to maximize its binding affinity. The results of the optimizer are used to predict beneficial growth vectors on the ligand, and good agreement is found between the predictions from the optimizer and a more rigorous free energy calculation, with a Spearman's rank order correlation of 0.59. The advantage of the method presented here is the significant speed up of over 10-fold compared to traditional free energy calculations and sublinear scaling with the number of growth vectors assessed. Where experimental data were available, mutations from hydrogen to a methyl group at sites highlighted by the optimizer were calculated with MBAR, and the mean unsigned error between experimental and calculated values of the binding free energy was 0.83 kcal/mol.
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Affiliation(s)
- Alexander D Wade
- TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - David J Huggins
- Tri-Institutional Therapeutics Discovery Institute, Belfer Research Building, 413 East 69th Street, 16th Floor, Box 300, New York, United States.,Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065, United States
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7
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Cole DJ, Mones L, Csányi G. A machine learning based intramolecular potential for a flexible organic molecule. Faraday Discuss 2020; 224:247-264. [DOI: 10.1039/d0fd00028k] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here, we employ the kernel regression machine learning technique to construct an analytical potential that reproduces the quantum mechanical potential energy surface of a small, flexible, drug-like molecule, 3-(benzyloxy)pyridin-2-amine.
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Affiliation(s)
- Daniel J. Cole
- School of Natural and Environmental Sciences
- Newcastle University
- Newcastle upon Tyne NE1 7RU
- UK
| | - Letif Mones
- Engineering Laboratory
- University of Cambridge
- Cambridge CB2 1PZ
- UK
| | - Gábor Csányi
- Engineering Laboratory
- University of Cambridge
- Cambridge CB2 1PZ
- UK
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8
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Wade AD, Huggins DJ. Optimization of Protein-Ligand Electrostatic Interactions Using an Alchemical Free-Energy Method. J Chem Theory Comput 2019; 15:6504-6512. [PMID: 31584802 PMCID: PMC7007198 DOI: 10.1021/acs.jctc.9b00976] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
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We present an explicit solvent alchemical free-energy method for
optimizing the partial charges of a ligand to maximize the binding
affinity with a receptor. This methodology can be applied to known
ligand–protein complexes to determine an optimized set of ligand
partial atomic changes. Three protein–ligand complexes have
been optimized in this work: FXa, P38, and the androgen receptor.
The sets of optimized charges can be used to identify design principles
for chemical changes to the ligands which improve the binding affinity
for all three systems. In this work, beneficial chemical mutations
are generated from these principles and the resulting molecules tested
using free-energy perturbation calculations. We show that three quarters
of our chemical changes are predicted to improve the binding affinity,
with an average improvement for the beneficial mutations of approximately
1 kcal/mol. In the cases where experimental data are available, the
agreement between prediction and experiment is also good. The results
demonstrate that charge optimization in explicit solvent is a useful
tool for predicting beneficial chemical changes such as pyridinations,
fluorinations, and oxygen to sulfur mutations.
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Affiliation(s)
- Alexander D Wade
- TCM Group, Cavendish Laboratory , University of Cambridge , 19 J J Thomson Avenue , Cambridge CB3 0HE , U.K
| | - David J Huggins
- TCM Group, Cavendish Laboratory , University of Cambridge , 19 J J Thomson Avenue , Cambridge CB3 0HE , U.K.,Tri-Institutional Therapeutics Discovery Institute , Belfer Research Building, 413 East 69th Street, 16th Floor, Box 300 , New York 10021 , United States.,Department of Physiology and Biophysics , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
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9
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Wade AD, Rizzi A, Wang Y, Huggins DJ. Computational Fluorine Scanning Using Free-Energy Perturbation. J Chem Inf Model 2019; 59:2776-2784. [PMID: 31046267 DOI: 10.1021/acs.jcim.9b00228] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We present perturbative fluorine scanning, a computational fluorine scanning approach using free-energy perturbation. This method can be applied to molecular dynamics simulations of a single compound and make predictions for the best binders out of numerous fluorinated analogues. We tested the method on nine test systems: renin, DPP4, menin, P38, factor Xa, CDK2, AKT, JAK2, and androgen receptor. The predictions were in excellent agreement with more rigorous alchemical free-energy calculations and in good agreement with experimental data for most of the test systems. However, the agreement with experiment was very poor in some of the test systems, and this highlights the need for improved force fields in addition to accurate treatment of tautomeric and protonation states. The method is of particular interest due to the wide use of fluorine in medicinal chemistry to improve binding affinity and ADME properties. The promising results on this test case suggest that perturbative fluorine scanning will be a useful addition to the available arsenal of free-energy methods.
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Affiliation(s)
- Alexander D Wade
- TCM Group, Cavendish Laboratory , University of Cambridge , 19 J J Thomson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Andrea Rizzi
- Tri-Institutional Training Program in Computational Biology and Medicine , New York , New York 10065 , United States.,Computational and Systems Biology Program , Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center , New York , New York 10065 , United States
| | - Yuanqing Wang
- Physiology, Biophysics, and System Biology Program , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
| | - David J Huggins
- TCM Group, Cavendish Laboratory , University of Cambridge , 19 J J Thomson Avenue , Cambridge CB3 0HE , United Kingdom.,Tri-Institutional Therapeutics Discovery Institute , Belfer Research Building , 413 East 69th Street, 16th Floor , Box 300, New York , New York 10021 , United States.,Department of Physiology and Biophysics , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
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10
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Cole DJ, Cabeza de Vaca I, Jorgensen WL. Computation of protein-ligand binding free energies using quantum mechanical bespoke force fields. MEDCHEMCOMM 2019; 10:1116-1120. [PMID: 31391883 DOI: 10.1039/c9md00017h] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 02/26/2019] [Indexed: 12/17/2022]
Abstract
A quantum mechanical bespoke molecular mechanics force field is derived for the L99A mutant of T4 lysozyme and used to compute absolute binding free energies of six benzene analogs to the protein. Promising agreement between theory and experiment highlights the potential for future use of system-specific force fields in computer-aided drug design.
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Affiliation(s)
- Daniel J Cole
- School of Natural and Environmental Sciences , Newcastle University , Newcastle upon Tyne NE1 7RU , UK .
| | - Israel Cabeza de Vaca
- Department of Chemistry , Yale University , New Haven , Connecticut 06520-8107 , USA
| | - William L Jorgensen
- Department of Chemistry , Yale University , New Haven , Connecticut 06520-8107 , USA
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11
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Kannan S, Tan DSW, Verma CS. Effects of Single Nucleotide Polymorphisms on the Binding of Afatinib to EGFR: A Potential Patient Stratification Factor Revealed by Modeling Studies. J Chem Inf Model 2018; 59:309-315. [DOI: 10.1021/acs.jcim.8b00491] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Srinivasaraghavan Kannan
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, 07-01 matrix, Singapore 138671, Singapore
| | - Daniel Shao-Weng Tan
- Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore
- Cancer Stem Cell Biology, Genome Institute of Singapore, 60 Biopolis Street, 02-01, Singapore 138672, Singapore
| | - Chandra Shekhar Verma
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, 07-01 matrix, Singapore 138671, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
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12
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Huggins DJ, Biggin PC, Dämgen MA, Essex JW, Harris SA, Henchman RH, Khalid S, Kuzmanic A, Laughton CA, Michel J, Mulholland AJ, Rosta E, Sansom MSP, van der Kamp MW. Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1393] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- David J. Huggins
- TCM Group, Cavendish Laboratory University of Cambridge Cambridge UK
- Unilever Centre, Department of Chemistry University of Cambridge Cambridge UK
- Department of Physiology and Biophysics Weill Cornell Medical College New York NY
| | | | - Marc A. Dämgen
- Department of Biochemistry University of Oxford Oxford UK
| | - Jonathan W. Essex
- School of Chemistry University of Southampton Southampton UK
- Institute for Life Sciences University of Southampton Southampton UK
| | - Sarah A. Harris
- School of Physics and Astronomy University of Leeds Leeds UK
- Astbury Centre for Structural and Molecular Biology University of Leeds Leeds UK
| | - Richard H. Henchman
- Manchester Institute of Biotechnology The University of Manchester Manchester UK
- School of Chemistry The University of Manchester Oxford UK
| | - Syma Khalid
- School of Chemistry University of Southampton Southampton UK
- Institute for Life Sciences University of Southampton Southampton UK
| | | | - Charles A. Laughton
- School of Pharmacy University of Nottingham Nottingham UK
- Centre for Biomolecular Sciences University of Nottingham Nottingham UK
| | - Julien Michel
- EaStCHEM school of Chemistry University of Edinburgh Edinburgh UK
| | - Adrian J. Mulholland
- Centre of Computational Chemistry, School of Chemistry University of Bristol Bristol UK
| | - Edina Rosta
- Department of Chemistry King's College London London UK
| | | | - Marc W. van der Kamp
- Centre of Computational Chemistry, School of Chemistry University of Bristol Bristol UK
- School of Biochemistry, Biomedical Sciences Building University of Bristol Bristol UK
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13
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Mena-Ulecia K, Gonzalez-Norambuena F, Vergara-Jaque A, Poblete H, Tiznado W, Caballero J. Study of the affinity between the protein kinase PKA and homoarginine-containing peptides derived from kemptide: Free energy perturbation (FEP) calculations. J Comput Chem 2018; 39:986-992. [PMID: 29399821 DOI: 10.1002/jcc.25176] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 12/05/2017] [Accepted: 01/13/2018] [Indexed: 12/28/2022]
Abstract
Protein kinases (PKs) discriminate between closely related sequences that contain serine, threonine, and/or tyrosine residues. Such specificity is defined by the amino acid sequence surrounding the phosphorylatable residue, so that it is possible to identify an optimal recognition motif (ORM) for each PK. The ORM for the protein kinase A (PKA), a well-known member of the PK family, is the sequence RRX(S/T)X, where arginines at the -3 and -2 positions play a key role with respect to the primed phosphorylation site. In this work, differential affinities of PKA for the peptide substrate Kemptide (LRRASLG) and mutants that substitute the arginine residues by the unnatural peptide homoarginine were evaluated through molecular dynamics (MD) and free energy perturbation (FEP) calculations. The FEP study for the homoarginine mutants required previous elaboration of a CHARMM "arginine to homoarginine" (R2B) hybrid topology file which is available in this manuscript as Supporting Information. Mutants substituting the arginine residues by alanine, lysine, and histidine were also considered in the comparison by using the same protocol. FEP calculations allowed estimating the free energy changes from the free PKA to PKA-substrate complex (ΔΔGE→ES ) when Kemptide structure was mutated. Both ΔΔGS→ES values for homoarginine mutants were predicted with a difference below 1 kcal/mol. In addition, FEP correctly predicted that all the studied mutations decrease the catalytic efficiency of Kemptide for PKA. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Karel Mena-Ulecia
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Avenida República #275, Universidad Andres Bello, Santiago de Chile, Chile
| | - Fabian Gonzalez-Norambuena
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile
| | - Ariela Vergara-Jaque
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile
| | - Horacio Poblete
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile
| | - William Tiznado
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Avenida República #275, Universidad Andres Bello, Santiago de Chile, Chile
| | - Julio Caballero
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile
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